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Crystal structure of AtWRKY18 DNA-binding domain in complex with W-box DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 0.1 M buffer system 1 (Imidazole; MES monohydrate (acid) ) pH 6.5, 20% v/v PEG 500* MME and 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 4.41 72.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.788 α = 90 b = 112.788 β = 90 c = 101.664 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.85 39.88 97.6 0.136 0.139 0.999 21.03 23.9 7918 91.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3.03 69.1 2.242 0.691 1.4 25.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7Z0R 2.85 39.88 1.35 7693 385 97.15 0.2533 0.2508 0.2512 0.2995 0.2988 85.32
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 27.7586 f_angle_d 0.8363 f_chiral_restr 0.0509 f_plane_restr 0.0077 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 614 Nucleic Acid Atoms 609 Solvent Atoms 8 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement